## ---- echo = FALSE,hide=TRUE, message=FALSE,warning=FALSE---------------- devtools::load_all(".") ## ----libs, eval=TRUE, message=FALSE,warning=F---------------------------- library(TCGAbiolinks) library(SummarizedExperiment) library(DT) library(dplyr) ## ----tcgabiolinks-exp, eval=FALSE---------------------------------------- # query.exp <- GDCquery(project = "TCGA-LUSC", # data.category = "Transcriptome Profiling", # data.type = "Gene Expression Quantification", # workflow.type = "HTSeq - FPKM-UQ", # barcode = c("TCGA-34-5231-01","TCGA-77-7138-01")) # GDCdownload(query.exp) # exp <- GDCprepare(query = query.exp, # save = TRUE, # save.filename = "Exp_LUSC.rda", # summarizedExperiment = TRUE) ## ----tcgabiolinks-exp-obj, eval=TRUE------------------------------------- exp colData(exp) %>% as.data.frame %>% datatable(options = list(scrollX = TRUE), rownames = TRUE) assay(exp)[1:5,] %>% datatable (options = list(scrollX = TRUE), rownames = TRUE) rowRanges(exp) ## ----tcgabiolinks-met, eval=FALSE---------------------------------------- # query.met <- GDCquery(project = "TCGA-LUSC", # data.category = "DNA Methylation", # platform = "Illumina Human Methylation 450", # barcode = c("TCGA-34-5231-01A-21D-1818-05","TCGA-77-7138-01A-41D-2043-05")) # GDCdownload(query.met) # met <- GDCprepare(query = query.met, # save = TRUE, # save.filename = "DNAmethylation_LUSC.rda", # summarizedExperiment = TRUE) ## ----tcgabiolinks-met-obj, eval=TRUE------------------------------------- met colData(met) %>% as.data.frame %>% datatable(options = list(scrollX = TRUE), rownames = TRUE) assay(met)[1:5,] %>% datatable (options = list(scrollX = TRUE), rownames = TRUE) rowRanges(met) ## ----sessioninfo, eval=TRUE---------------------------------------------- sessionInfo()